Justice Brett Kavanaugh, however, said the occupancy cap "indisputably discriminates against religion, and such discrimination violates the First Amendment."
"The church would suffer irreparable harm from not being able to hold services on Pentecost Sunday in a way that comparable secular businesses and persons can conduct their activities," he said in his dissent.
"The basic constitutional problem is that comparable secular businesses are not subject to a 25% occupancy cap, including factories, offices, supermarkets, restaurants, retail stores, pharmacies, shopping malls, pet grooming shops, bookstores, florists, hair salons, and cannabis dispensaries," he continued.
Kavanaugh said the state must offer a "compelling justification" to distinguish between religious worship services and "the litany of other secular businesses that are not subject to an occupancy cap."
"California has not shown such a justification," he said, noting the importance of the church's willingness to abide by state rules that apply to comparable secular business, including social distancing and hygiene rules.
"I would grant the Church's requested temporary injunction because California's latest safety guidelines discriminate against places of worship and in favor of comparable secular businesses. Such discrimination violates the First Amendment," he said.
Kavanaugh's dissent was joined by Justices Clarence Thomas and Neil Gorsuch. Justice Samuel Alito dissented but did not join the opinion.
The court rejected a different appeal from two Chicago-area churches that challenged a 10-person limit on attendees at religious services. Before the court took action, Gov. Jay Pritzker increased the limit to 100 attendees per service.
The churches, Elim Romanian Pentecostal Church of Chicago and Logos Baptist Ministries of Niles, Ill., had both sought to open ahead of the Christian holy day of Pentecost.
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